Skip to main content Accessibility help

We use cookies to distinguish you from other users and to provide you with a better experience on our websites. Close this message to accept cookies or find out how to manage your cookie settings.

Close cookie message
×
Hostname: page-component-76fb5796d-vvkck Total loading time: 0 Render date: 2024-04-26T05:21:31.069Z Has data issue: false hasContentIssue false

9 - Rhizosphere carbon flow: a driver of soil microbial diversity?

Published online by Cambridge University Press:  17 September 2009

By
D. B. Standing ,
J. I. Rangel Castro ,
J. I. Prosser ,
A. Meharg  and
K. Killham
Edited by
Richard Bardgett ,
Michael Usher  and
David Hopkins
D. B. Standing
Affiliation:
University of Aberdeen
J. I. Rangel Castro
Affiliation:
University of Aberdeen
J. I. Prosser
Affiliation:
University of Aberdeen
A. Meharg
Affiliation:
University of Aberdeen
K. Killham
Affiliation:
University of Aberdeen
Richard Bardgett
Affiliation:
Lancaster University
Michael Usher
Affiliation:
University of Stirling
David Hopkins
Affiliation:
University of Stirling
Get access

Summary

SUMMARY

  1. Microorganisms play an essential role in modulating the fluxes of organic carbon and nutrients in soil. However, their diversity and functional significance are largely unknown. Recent technical developments in molecular, chemotaxonomic and physiological techniques complement traditional techniques and can now enable us to investigate the linkage between rhizosphere carbon flow, microbial diversity and soil function.

  2. Reporter gene systems provide an important method for resolution of rhizosphere carbon flow. Their greatest advantage is that they can be used in situ without uncoupling the plant–microbial interaction vital to maintaining both quantity and quality of carbon flow.

  3. Any consideration of rhizosphere carbon flow and soil microbial diversity should not only include substrate carbon flow and trophic interactions, but also the role of signal molecules, especially in terms of controlling rhizosphere community structure, diversity and function.

  4. Little is known of carbon flow in natural systems. Ecosystem function and, specifically, carbon-cycling pathways can be determined by lipid analysis or nucleic acid stable isotope probing (SIP) using 13C incorporated into microbial biomass. The ability to ascertain which components of the biomass are being enriched in root-derived carbon enables an understanding of how rhizosphere carbon drives microbial diversity.

  5. Changes in 16S rDNA sequence diversity and relative abundance provide indications of which organisms are responding to changing conditions and SIP analysis of mRNA allows for assessment of their activity, and thus may be used to follow changes in the microbial community during rhizosphere development.

Type
Chapter
Information
Biological Diversity and Function in Soils , pp. 154 - 168
Publisher: Cambridge University Press
Print publication year: 2005

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Amann, R. I., Ludwig, W. & Schleifer, K.-H. (1995). Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiology Reviews, 59, 143–169Google ScholarPubMed
April, W. & Sims, R. C. (1990). Evaluation of the use of prairie grasses for stimulating polycyclic aromatic hydrocarbon treatment in soil. Chemosphere, 20, 253–265CrossRefGoogle Scholar
Arao, T. (1999). In situ detection of changes in soil bacterial and fungal activities by measuring 13C incorporation into soil phospholipid fatty acids from 13C acetate. Soil Biology and Biochemistry, 31, 1015–1020CrossRefGoogle Scholar
Bauer, W. D. & Teplitski, M. (2001). Can plants manipulate bacterial quorum sensing?Australian Journal of Plant Physiology, 28, 913–921Google Scholar
Borneman, J., Skroch, P. W., O'Sullivan, K. M., et al. (1996). Molecular microbial diversity of an agricultural soil in Wisconsin. Applied and Environmental Microbiology, 62, 1935–1943Google ScholarPubMed
Borneman, J. & Triplett, E. W. (1997). Molecular microbial diversity in soils from eastern Amazonia: evidence for unusual microorganisms and microbial population shifts associated with deforestation. Applied and Environmental Microbiology, 63, 2647–2653Google ScholarPubMed
Boschker, H. T. S., Nold, S. C., Wellsbury, P., et al. (1998). Direct linking of microbial populations to specific biogeochemical processes by C-13-labelling of biomarkers. Nature, 392, 801–805CrossRefGoogle Scholar
Bowen, G. D. & Rovira, A. D. (1991). The rhizosphere, the hidden half of the hidden half. Plant Roots: the Hidden Half (Ed. by , Y. Waisel, , A. Eshel & , U. Kafkafi), pp. 641–669. New York: Marcel Dekker
Bull, I., Parekh, N., Ineson, P. & Evershed, R. E. (2000). Detection and classification of atmospheric methane oxidizing bacteria in the soil. Nature, 405, 175–178CrossRefGoogle ScholarPubMed
Bürgmann, H., Widmer, F., Sigler, W. V. & Zeyer, J. (2003). mRNA extraction and reverse transcription-pcr protocol for detection of nifH gene expression by Azotobacter vinelandii in soil. Applied and Environmental Microbiology, 69, 1928–1935CrossRefGoogle ScholarPubMed
Cha, C., Gao, P., Chen, Y.-C., Shaw, P. D. & Farrand, S. K. (1998). Production of acyl-homoserine lactone quorum-sensing signals by Gram-negative plant-associated bacteria. Molecular Plant Microbe Interactions, 11, 1119–1129CrossRefGoogle ScholarPubMed
Duineveld, B. M., Rosado, A. S., Elsas, J. D. & Veen, J. A. (1998). Analysis of the dynamics of bacterial communities in the rhizosphere of the Chrysanthemum via denaturing gradient gel electrophoresis and substrate utilization patterns. Applied and Environmental Microbiology, 64, 4950–4957Google ScholarPubMed
Elasri, M., Delorme, S., Lemanceau, P., et al. (2001). Acyl-homoserine lactone production is more common among plant-associated Pseudomonas spp. than among soilborne Pseudomonas spp. Applied and Environmental Microbiology, 67, 1198–1209CrossRefGoogle ScholarPubMed
Felske, A., Wolterink, A., Lis, R. & Akkermans, A. D. L. (1998). Phylogeny of the main bacterial 16S rRNA sequences in Drentse A grassland soils (The Netherlands). Applied and Environmental Microbiology, 64, 871–879Google Scholar
Hanson, R. S. & Hanson, T. E. (1996). Methanotrophic bacteria. Microbiology Reviews, 60, 439–471Google ScholarPubMed
Holmes, A. J., , Roslev P., , McDonald I. R., et al. (1999). Characterization of methanotrophic bacterial populations in soil showing atmospheric methane uptake. Applied and Environmental Microbiology, 65, 3312–3318Google ScholarPubMed
Kandeler, E., Tscherko, D., Bruce, K. D., et al. (2000). Structure and function of the soil microbial community in microhabitats of a heavy metal polluted soil. Biology and Fertility of Soils, 32, 390–400CrossRefGoogle Scholar
Killham, K. (1994). Soil Ecology, pp. 83–85. Cambridge: Cambridge University PressGoogle Scholar
Killham, K. & Yeomans, C. (2001). Rhizosphere carbon flow measurement and implications: from isotopes to reporter genes. Plant and Soil, 233, 91–96CrossRefGoogle Scholar
Kowalchuk, G. A., Buma, D. S., Boer, W., Klinkhamer, P. G. L. & Veen, J. A. (2002). Effects of above-ground plant species composition and diversity on the diversity of soil-borne microorganisms. Antonie van Leeuwenhoek International Journal of General and Molecular Microbiology, 81, 509–520CrossRefGoogle ScholarPubMed
Lagido, C., Pettitt, J., Porter, A. J. R., Paton, G. I. & Glover, L. A. (2001). Development and application of bioluminescent Caenorhabditis elegans as multicellular eukaryotic biosensors. FEBS Letters, 493, 36–39CrossRefGoogle ScholarPubMed
Marilley, L. & Aragno, M. (1999). Phylogenetic diversity of bacterial communities differing in degree of proximity of Lolium perenne and Trifolium repens roots. Applied Soil Ecology, 13, 127–136CrossRefGoogle Scholar
McCaig, A. E., Glover, L. A. & Prosser, J. I. (1999). Molecular analysis of bacterial community structure and diversity in unimproved and improved grass pastures. Applied and Environmental Microbiology, 65, 1721–1730Google ScholarPubMed
Meharg, A. A. & Killham, K. (1991). A novel method of quantifying rhizosphere carbon flow in the presence of soil microflora. Plant and Soil, 133, 111–116CrossRefGoogle Scholar
Normander, B. & Prosser, J. I. (2000). Bacterial origin and community composition in the barley phytosphere as a function of habitat and presowing conditions. Applied and Environmental Microbiology, 66, 4372–4377CrossRefGoogle ScholarPubMed
O'Donnell, A. G. (2001). Plants and fertilisers as drivers of change in microbial community structure and function in soil. Plant and Soil, 232, 135–145CrossRefGoogle Scholar
Paau, A. S. (1988). Formulations useful in applying beneficial microorganisms to seeds. Trends in Biotechnology, 6, 276–279CrossRefGoogle Scholar
Phillips, C. J., Paul, E. A. & Prosser, J. I. (2000). Quantitative analysis of ammonia oxidising bacterial using competitive PCR. FEMS Microbiology Ecology, 32, 167–175CrossRefGoogle Scholar
Pierson, E. A., Wood, D. W., Cannon, J. A., Blachere, F. M. & Pierson, L. S. III. (1998). Interpopulation signaling via N-acyl-homoserine lactones among bacteria in the wheat rhizosphere. Molecular Plant Microbe Interactions, 11, 1078–1084CrossRefGoogle Scholar
Priha, O., Grayston, S. J., Hiukka, R., Pennanen, T. & Smolander, A. (2001). Microbial community structure and characteristics of the organic matter in soils under Pinus sylvestris, Picea abies and Betula pendula at two forest sites. Biology and Fertility of Soils, 33, 17–24CrossRefGoogle Scholar
Raaijmakers, J. M., Bonsall, R. F. & Weller, D. M. (1999). Effect of population density of Pseudomonas fluorescens on production of 2,4-diacetylphloroglucinol in the rhizosphere of wheat. Phytopathology, 89, 470–475CrossRefGoogle ScholarPubMed
Radajewski, S., Ineson, P., Parekh, N. R. & Murrell, J. C. (2000). Stable-isotope probing as a tool in microbial ecology. Nature, 403, 646–649CrossRefGoogle ScholarPubMed
Sait, M., Hugenholtz, P. & Janssen, P. H. (2002). Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys. Environmental Microbiology, 4, 654–666CrossRefGoogle ScholarPubMed
Salmond, G. P. C., Bycroft, B. W., Stewart, G. S. A. B. & Williams, P. (1995). The bacterial ‘enigma’: cracking the code of cell–cell communication. Molecular Microbiology, 16, 615–624CrossRefGoogle ScholarPubMed
Schell, M. A. (1993). Molecular biology of the LysR family of transcriptional regulators. Annual Reviews in Microbiology, 47, 597–626CrossRefGoogle ScholarPubMed
Spiers, A. J., Buckling, A. & Rainey, P. B. (2000). The causes of Pseudomonas diversity. Microbiology, 146, 2345–2350CrossRefGoogle ScholarPubMed
Stead, P., Rudd, B. A. M., Bradshaw, H., Noble, D. & Dawson, M. J. (1996). Induction of phenazine biosynthesis in cultures of Pseudomonas aeruginosa by l-N-(3-oxohexanoyl)homoserine lactone. FEMS Microbiology Letters, 140, 15–22CrossRefGoogle ScholarPubMed
Stephen, J. R., McCaig, A. E., Smith, Z., Prosser, J. I. & Embley, T. M. (1996). Molecular diversity of soil and marine 16S rRNA gene sequences related to beta-subgroup ammonia-oxidizing bacteria. Applied and Environmental Microbiology, 62, 4147–4154Google ScholarPubMed
Teplitski, M., Robinson, J. B. & Bauer, W. D. (2000). Plants secrete substances that mimic bacterial N-acyl homoserine lactone signal activities and affect population density-dependent behaviours in associated bacteria. Molecular Plant Microbe Interactions, 13, 637–648CrossRefGoogle ScholarPubMed
Torsvik, V., Sorheim, R. & Goksoyr, J. (1996). Total bacterial diversity in soil and sediment communities: a review. Journal of Industrial Microbiology, 17, 170–178CrossRefGoogle Scholar
Turner, J. T. & Backman, P. A. (1991). Factors relating to peanut yield increases following Bacillus subtilis seed treatment. Plant Diseases, 75, 347–353CrossRefGoogle Scholar
Vilchez, S., Molina, L., Ramos, C. & Ramos, J. L. (2000). Proline catabolism by Pseudomonas putida: cloning, characterization, and expression of the put genes in the presence of root exudates. Journal of Bacteriology, 182, 91–99CrossRefGoogle ScholarPubMed
Walton, B. T. & Anderson, T. A. (1990). Microbial degradation of trichloroethylene in the rhizosphere: potential application to biological remediation of waste sites. Applied and Environmental Microbiology, 56, 1012–1016Google ScholarPubMed
Whiteley, M., Lee, K. M. & Greenberg, E. P. (1999). Identification of genes controlled by quorum sensing in Pseudomonas aeruginosa. Proceedings of the National Academy of Sciences USA, 96, 13 904–13 909CrossRefGoogle ScholarPubMed
Winson, M. K., Swift, S., Fish, L., et al. (1998a). Construction and analysis of lux CDABE-based plasmid sensors for investigating N-acyl homoserine lactone-mediated quorum sensing. FEMS Microbiology Letters, 163, 185–192CrossRefGoogle Scholar
Winson, M. K., Swift, S., Hill, P. J., et al. (1998b). Engineering the lux CDABE genes from Photorhabdus luminescens to provide a bioluminescent reporter for constitutive and promoter probe plasmids and mini-Tn5 constructs. FEMS Microbiology Letters, 163, 193–202CrossRefGoogle Scholar
, Wood D. W. & , Pierson L. S. (1996). The phzI gene of Pseudomonas aureofaciens 30–84 is responsible for the production of a diffusible signal required for phenazine antibiotic production. Gene, 168, 49–53CrossRefGoogle Scholar
Yang, C.-H. & Crowley, D. E. (2000). Rhizosphere microbial community structure in relation to root location and plant iron nutritional status. Applied and Environmental Microbiology, 66, 345–351CrossRefGoogle ScholarPubMed
Yeomans, C., Porteous, F., Paterson, E., Meharg, A. A. & Killham, K. (1999). Use of lux marked rhizobacteria as reporters of rhizosphere C-flow. FEMS Microbiology Letters, 176, 79–83CrossRefGoogle Scholar
Zhou, J. Z., Davey, M. E., Figueras, J. B., et al. (1997). Phylogenetic diversity of a bacterial community determined from Siberian tundra soil DNA. Microbiology, 143, 3913–3919CrossRefGoogle ScholarPubMed
Zhu, J., Oger, P. M., Schrammeijer, B., et al. (2000). The bases of crown gall tumorigenesis. Journal of Bacteriology, 182, 3885–3895CrossRefGoogle ScholarPubMed

Save book to Kindle

To save this book to your Kindle, first ensure coreplatform@cambridge.org is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about saving to your Kindle.

Note you can select to save to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be saved to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

Find out more about the Kindle Personal Document Service.

Available formats
×

Save book to Dropbox

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Dropbox.

Available formats
×

Save book to Google Drive

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Google Drive.

Available formats
×